Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Illegal character in hostname at index 9

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    Genevieve Brandt (she/her)

    Hi Bob Ye Lindo Nkambule,

    Thanks for writing into the forum with this issue! Hopefully we can help out and we can get this resolved for you.

    You're right that the underscores are causing an issue. Underscores are not allowed for URI host names (aka your gs://daly_schema2_gnomad_subset_vds is a URI host). GATK follows the URI spec for this, which you can read more about it here: https://en.wikipedia.org/wiki/Hostname#Restrictions_on_valid_host_names.

    It's a legal Google Cloud bucket name, but when you refer to the bucket in a URI, it causes problems there. Ideally, you can contact the owner of the bucket and they can rename the bucket to use hyphens instead of underscores. 

    Let me know if you have any other questions about this.

    Best,

    Genevieve

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